Sometimes entire species vanish almost unnoticed on the ebb of history.

And sometimes — to widespread astonishment — those same species ride the currents of conservation back home again.

Humans have exacted a terrible toll on our region’s marine life over the past 150 years, through commercial whaling, reckless overfishing, and bounties, culls, and commercial harvests of harbour seals and sea lions.

Without question, the ecological effect of those actions continues to be felt today.

But there are also signs that the Salish Sea — the shared inland waters of Juan de Fuca Strait, B.C.’s Strait of Georgia, and Washington state’s Puget Sound — is stirring and, who knows, may once again approach its former greatness.

Thanks to conservation efforts, one marine mammal after another is making a dramatic comeback, their presence providing the biggest reason for hope across an ecosystem spanning 7,000 square kilometres.

Steller sea lions have thrived since the federal government afforded them protection in 1970 — with new abundance estimates pegging their population at 48,000 animals in winter on the B.C. coast.

The breeding population had dipped to an estimated 3,400 animals before their protection.

Similarly, harbour seals today total an estimated 105,000 animals, one of the densest such populations on earth, compared with fewer than 15,000 in the late 1960s.

All those nutritious blubbery bodies are proving irresistible to mammal-eating killer whales known as “transients.”

About 120 transients are known to visit the Strait of Georgia, surpassing an endangered population of fish-eating resident killer whales thought to number 88 in three pods — a story that sadly runs counter to the others.

Humpback whales are now found year-round on our coast, while a genetically distinct population of grey whales with unique feeding habits makes regular forays off Vancouver.

For the first time in memory, fin whales — the second largest animal on earth, after the blue whale — have been spotted near the north end of the Strait of Georgia past Campbell River.

Hundreds of Pacific white-sided dolphins now call the strait home, including Howe Sound — an area that is experiencing an ecological reawakening after the treatment of mine effluent, the closure of a pulp mill, and the restoration efforts of local streamkeepers.

And the car-sized northern elephant seal — once reduced to fewer than 100 individuals — now numbers up to 200,000 from Mexico to Alaska.

The dramatic return of so many marine mammals at the top of the food chain also suggests good productivity at the bottom, for predators cannot thrive without the fish and smaller creatures upon which they prey. But there are also dozens of species that are not doing as well in the Salish Sea, a complex and poorly understood ecosystem.

A study by the SeaDoc Society — based in the San Juan Islands and affiliated with the Wildlife Health Center at the University of California, Davis — has found a total of 113 species to be threatened, endangered, or candidates for listing by state, provincial or federal levels of government.

Included in the most recent count: 56 species of bird such as the western grebe and Brandt’s cormorant; 37 fish such as salmon and rockfish; 15 mammals; three invertebrates; and two reptiles.

Those 113 threatened species are almost double from the 64 identified two years ago, a reflection, in part, of a growing awareness among government managers who officially list species as being at risk.

It’s a critical step in the recovery process.

As marine mammals have shown, sometimes the public policy fixes are simple. All it took was for governments to formally put an end to the killing to allow populations to begin to recover.

Other species are not so easy.

The challenges are greater with, say, salmon, whose survival depends equally on protected spawning habitat far upstream from the Salish Sea, or birds that depend on nesting grounds as far north as the Arctic.Scott Wallace is a sustainable fisheries analyst with the David Suzuki Foundation who studied changes in the ecology of the Salish Sea ecosystem over a century as part of his PhD thesis 15 years ago at the University of British Columbia.

Pointing to depressed stocks of groundfish species such as rockfish, lingcod, halibut, and Pacific cod in the strait, he questions whether the Salish Sea will ever achieve the productivity of pre-European contact.

Still, there remains much to be celebrated. “It is by no means a dead sea,” he emphasized. “It’s a thriving live ecosystem, still extremely productive — an incredible resource on the back door of a major city.”

There are many factors conspiring against a comeback, some direct, such as fishing and habitat destruction, and some more subtle, like the long-term threats of climate change.

Ocean warming is predicted to reduce the amount of oxygen for fish while pushing more southerly species such as the ravenous Humboldt squid further north — with potentially dire consequences for local marine stocks.

Warming rivers will become increasingly inhospitable to spawning salmon and oolichan.

Increased acidification of the oceans under climate change will compromise marine productivity at the base of the food chain.

An expanding human population is exacting an ever-greater toll — pollution, shoreline development, noise and harassment from marine traffic, including from navy sonar and explosions.

And, of course, there is the age-old competition between human and wild predators for the same prey fish.

“There’s been a conflict almost as long as people have been catching fish,” said Andrew Trites, director of the marine mammal research unit in the Fisheries Centre at UBC.

“Society has to decide how they want these fish allocated.”

Whereas in the past we shot species such as seals and sea lions and captured killer whales for public display, including at the Vancouver Aquarium, today governments increasingly balance the needs of nature as well as humans.

That process has already begun in the Salish Sea for the endangered southern resident killer whales.

Canada’s federal fisheries department and the U.S. National Oceanic and Atmospheric Administration are holding a series of meetings aimed at managing chinook salmon stocks to ensure the needs of killer whales are met.

Co-managing species that share international waters is the wave of the future, says Rob Williams, a research fellow with the sea mammal research unit at the University of St. Andrews in Scotland who works extensively on the B.C. coast.

Canada and the U.S. have the chance to show global leadership through the conservation of resident killer whales.

“That would be progressive by any country’s standards, making sure that a valued and critically endangered predator gets access to prey,” he said. “If we can do that with killer whales, we should be doing it with sharks, seabirds, and all sorts of things.”

And killer whales have big appetites, especially for the largest species of wild Pacific salmon, the chinook, according to a study published in November 2011 in the online scientific journal PLoS ONE.

The study concluded it takes the equivalent of 660 chinook a day to feed all the southern residents, which consume between 12 per cent and 23 per cent of the Fraser River’s runs.

If their population recovers to 155 animals by 2029 — the goal of a U.S. recovery strategy — the whales’ need for food would increase by up to 75 per cent, the study estimates.

While humans may have to forgo some of their catch to help killer whales in the short term, the ultimate objective is to produce more salmon for all through measures such as habitat enhancement, including protection of critical spawning habitat and restoration of other stretches damaged over the generations.

“Especially with salmon, we have to make more,” says Williams, the study’s lead author.Competition between humans and marine mammals does not stop at salmon, but extends all the way down the food chain in the Salish Sea to include species such as herring and tiny, shrimp-like krill.

Ottawa sets an annual catch limit of 500 tonnes on krill, a fishery is conducted at night with beam trawls when the schools rise closer to the surface.

The U.S. banned krill fishing on the West Coast in 2009 within its 200-mile territorial limit as a way to provide more food for marine life, including endangered fish and birds.

Krill is used by places such as the Vancouver Aquarium and California’s Monterey Bay Aquarium, which gets its supply from Canada.

Meanwhile, herring roe goes to Japan, with the carcasses going to reduction for purposes such as fishmeal.

Some say it is folly to harvest the ecological underpinnings of the Salish Sea, especially for non-human consumption.

“That is a disgrace, a damn shame,” said professor Dan Pauly of UBC’s Fisheries Centre. “There is not much as good as herring, smoked or fileted or pickled.”

Lisa Mijacika, herring coordinator for the federal fisheries department, said the strait’s stocks are estimated at 138,000 tonnes, of which 18,000 tonnes, or 13 per cent, were designated this year to sectors such as commercial roe, food and bait.

“It’s reasonably conservative in our view,” she said, noting a 20-per-cent catch would have been sustainably justified.

Wallace, of the David Suzuki Foundation, sits as the conservation representative on a federal herring planning committee and says the krill fishery is not a conservation risk at current levels and that he considers the herring fishery to be “relatively well managed.”

Recovering herring stocks are a symbol of the improving ecological health of Howe Sound.

Volunteer streamkeepers are credited with wrapping pilings with plastic to protect herring roe from toxic creosote, while the shutdown of the Woodfibre pulp mill in 2006 and construction of a plant in 2005 to treat toxic mine drainage on Britannia Creek resulted in the return of about two dozen pink salmon last year.

Black rockfish vanished from our local waters “in the days of The Sun Salmon Derby,” said Jeff Marliave, the aquarium’s vice-president of science. The derby ran for more than four decades before declining salmon runs in the 1980s quietly put an end to it.

“You couldn’t help but catch them, they’re such aggressive lure-strikers. Easier to catch than coho.”

Now, Marliave said, there are signs that black rockfish transplanted by the aquarium from 1997 to 2006 at Lighthouse Park in West Vancouver are breeding and helping to restore the population.

“We’ve got herring, we’ve got feed,” he said. “It has to do with the whole ecology. We have something big happening locally.”

As scientists grapple to understand changes in the Salish Sea, it’s important for the public to appreciate the ecosystem is complicated and rarely as obvious as it might seem.

Fishermen who curse harbour seals for stealing salmon off their lines may not realize that seals’ year-round diet can also benefit stocks of the prized catch.

One study in the Strait of Georgia found that while harbour seals are opportunistic predators, hake — a predator of young salmon — and herring account for about 75 per cent of their total diet. And new research is underway at UBC to better determine their eating habits.

Other studies are shedding more light on the complex and unexpected interactions between marine life.

When seals were culled in Alaska’s Copper River delta in the 1960s to reduce predation on salmon, it resulted not in increased salmon but a failure of the razor-clam fishery. The shortage of predators allowed the starry flounder, another primary element of seals’ diet, to feed on the clams unchecked.

Similarly, while sea otters off Vancouver Island consume the same sea urchins enjoyed by humans, the harvest of urchins allows for the growth of kelp beds that enhance the overall marine diversity.

“We shouldn’t trust our eyes because there is a lot happening below the surface that we don’t know,” says Pauly of UBC’s Fisheries Centre. Trites, his colleague at the Centre, concurs: “Often there are indirect effects that we cannot anticipate.”

While the interconnection between marine mammals and their prey may fall off the radar for most of us, the link could not be more evident to John Ford, a federal biologist with the cetacean research program based in Nanaimo.

Looking out across Departure Bay, he can watch both Steller and California sea lions swimming to feed on spawning herring at nearby Piper’s Lagoon.

On another day, the tides will turn and the sea lions will find themselves prey for the transient killer whales.

Rare in the Strait of Georgia as recently as the mid-1970s, the transients have been increasing steadily at two to three per cent per year.

In comparison, the 88 southern resident killer whales are down from 98 animals in 1995, a decline that coincided with a period of low chinook salmon runs.

In 2001, there were just 80 residents — in human terms, about the size of a block party.

Transients are highly mobile, making it difficult for scientists to identify critical habitat. But they can now be found here all year, peaking in late August and September when harbour seal pups are weaning and most numerous.

Some scientific observers ask what took them so long to discover the easy meal options afforded in the Salish Sea.

“I was puzzled, for years we had this big increase in harbour seals, and the transients didn’t seem to catch on right away,” said Barrett-Lennard of the Vancouver Aquarium. “Now it’s easy pickings. It’s no longer the haven for harbour seals that it once was. For a while they didn’t have large predators. Now, they’re on their toes again.”

The transients are not the only whale comeback success story in the Salish Sea.

Humpbacks have been increasing in B.C. waters at four to six per cent per year, with the population locally estimated at 2,600 individuals, part of a north Pacific population estimated at 18,000. The population is thought to have dropped to as low as 1,500 animals in the 1960s.

Commercial whaling occurred in local waters in two waves, from the late 1860s to early 1870s and again in 1907. Just eight whales rendered in Saanich Inlet in 1868 yielded 45,500 litres of oil.

Along the outer coast, five whaling stations killed at least 24,250 whales from 1907 to 1967, when whaling ended.

Today, humpbacks have made a strong recovery. Sightings of the animals are routine in the Strait of Georgia, including off Victoria, the Gulf Islands, Nanaimo and Sunshine Coast.

While the vast majority of B.C.’s humpbacks migrate to Hawaii or Mexico during the winter, individuals are present off our coast all year, with numbers peaking in late summer and fall.

As long as these whales have food and clean habitat without undue harassment and noise from vessel traffic they should continue to thrive, said Ford, of federal fisheries.

However, humpbacks return each year to within a few kilometres of their feeding grounds, meaning they are slow to recolonize areas where they were depleted by commercial whaling. And females bringing back young from tropical waters will introduce them to traditional grounds, behaviour that’s led to about 50 humpbacks now found off Telegraph Cove on northeastern Vancouver Island.

Another success story are the grey whales in the eastern north Pacific, which have rebounded after a setback between 1999 and 2000.

The population dropped by up to 25 per cent that year, with strandings commonplace along their migration route, including on the beaches off White Rock, Tsawwassen and the Gulf Islands.

Scientists blamed the problem on poor feeding conditions in the Bering Sea, where excessive ice prevented the whales from accessing their shallow feeding grounds.

“They started their migration in poor condition and ran out of gas on the way back,” said Ford, speculating they swam into shallow, muddy Boundary Bay at that time searching for food. “Some didn’t make it and wound up on the beach.”

Current numbers are estimated at 18,000 to 20,000, and researchers are finding some startling genetic and behavioural differences in the local population.Jim Darling, a marine biologist with B.C.’s Pacific WildLife Foundation, said that rather than migrate to Arctic waters with the rest, about 200 whales — or one per cent of the population — remain along the coast between northern California and southeastern Alaska.

The west coast of Vancouver Island is a key feeding area for this group, although individuals have turned up in Howe Sound, False Creek, and several can linger for months in Boundary Bay.

Genetic tests of mitochondrial DNA passed on by mothers to offspring show B.C.’s grey whales are “genetically distinct” and should be managed separately from the overall population, Darling said, a finding that has implications for the whaling aspirations of aboriginal groups such as the Makah of the Olympic Peninsula and Nuu-chah-nulth of Vancouver Island.

In effect, B.C.’s grey whales have a culture that is distinct from the larger population.

“My hunch is they’ve been here for as long as there’s been a coast,” Darling said. “Their knowledge and behaviour have been passed down from one generation to the next.”

After studying whales since the 1970s, Darling laments that management decisions on whales continue to be based on limited knowledge at best and often no knowledge at all.

“We tend to think of them as the same, clones of each other, think of them as numbers, but that is not the case.”

Despite the myriad of management dilemmas and ecological uncertainties swirling about the Salish Sea, know there is nothing as visible or demonstrable of humanity’s passion for the oceans as the return of the whales.

One need only recall the public and media frenzy that arose when a grey whale swam into False Creek in May 2010 and again off West Vancouver and Stanley Park in August that same year.

People thronged the seawall in a bid to catch a glimpse, some paddling, even swimming out for a closer look.

Whales fill us with hope.

If something so big can flourish here, maybe in time the smaller and less obvious parts of the puzzle can, too.

Their return to Vancouver gives us pause to consider past mistakes and the promise ahead for a vibrant Salish Sea, for marine life and all of us.

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